Recent surveys have found that a vast majority of users that run screen readers have JS enabled, not disabled. Granted, a screen reader does what its name implies: it reads the screen. If a screen reader doesn't know where to read, then it can't do its job. For instance, modal dialogs are probably a bad idea if you're looking to support those users, though including something like form validation probably isn't a terrible idea.
The idea is to keep items on the screen from changing too rapidly. If you update large elements of your UI frequently using JS, you're probably not going to get too great of a response from the screen reader community. On the other hand, if the majority of the JS is behind-the-scenes, then most screen reader users probably won't even notice that you're using scripts.
The list at the bottom of the link I provided above gives some great insight into the biggest problems that screen reader users face. Avoiding any situations where those scenarios might pop up (i.e.: visual CAPTCHAs, complex layouts, rapidly updated UI elements, etc.) will probably leave you in good shape.
And as always, download yourself a screen reader (there are plenty of free and open source readers available) to test out your software.
Good luck!